Wednesday, June 23, 2010

Well, the saga on "Freeing my father's publications" continues. I am now experimenting with posting papers by my father on a "personal" website dedicated to this task, since most/many journals allow one to post one's papers this way.

Since I am about to head out to a meeting, I am going to do the simple part first. Making a collection of as many of his papers as I can. I am posting these on a "Page" associated with this blog here, at least for now.

Here is the first:

Eisen HJ, Goodman HM. Growth hormone and phosphorylase activity in adipose tissue. Endocrinology. 1969 Feb;84(2):414-6. PMID: 4303531. I have a printed copy I made 10 or so years ago. I scanned it with my Fukitsu ScanSnap S1500M scanner and used the "convert to PDF with text" option. And this is what came out. Not perfect but not so bad.

Monday, June 21, 2010

Just thought I would post a few pics of the new Shields Oak Grove path/tour in the Davis Arboretum. It is very very nice and looks like it will expand with more trails, etc. The pics do not do the place justice but I thought I would post anyway.

And alas things did not start out well today. At the suggestion of Linda Avey I looked at Academia.Edu to see if I could create a page there for my father. I guess I could have lied, but they ask for current institution/affiliation so I could not do that.

So I decided to start to try to download his papers from journal sites to use when I create some web site for him... not getting very far I note ... and getting a bit pissed off.

Available online apparently here. Published by The Endocrine Society which makes papers from 12 month old back to 1997 available for free online. But it does not make older papers available. What an inane policy. So I cannot (legally) get a PDF of this paper without paying for it? F*$cking brilliant. Glad though, that UC Davis is not paying for this as it should be available for free to everyone.

Sunday, June 20, 2010

Well, it is Father's Day. And inevitably I end up thinking about my father, who passed away in 1987. As part of wanting to keep the memories of my father alive, every Father's Day I end up thinking at least a little bit about my father's scientific work. He was an MD who did research at the NIH, focusing mostly on glucocorticoid receptor's and related topics.

But inevitably, as with most things in life, I got busy and never ended up finishing this activity. And so I am back to it again in 2010. And I am still struggling to do this. The fact that papers by my father, published some 20-40 years in the past, are still not all available is indicative in part of the broken state of scientific publishing. For example, many of his papers are available electronically, but are behind some pay wall from a publisher that limits access (I made a list of many of his papers here: CiteULike: Group Papers by my father, Howard J. Eisen)

I do not think that this is what NIH or taxpayers envisioned when they supported his work -for it to basically be lost due to greed. And as my brother pointed out in a comment on one of those posts from 2 years ago - since my father worked for the NIH his publications should be free anyway, in terms of government employees not being allowed to sign over copyright.

So I am going to at least do what I can to free them up and make them known. My main plan is to get PDFs of all the papers (some I can download, others I will have to scan myself), and create a "personal" website to distribute all of them. Hopefully these will get picked up by Google Scholar. And I am going to explore whether there are better ways to get these papers in the public domain. I am also going to try to do whatever else I can to get his work into the public domain - it seems like the least I can do to honor his memory.

Whether one agrees with his critiques or not, I hope that everyone can recognizes that one section on evolution is, well, awful. Wade writes

First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.

While Mr. Wade may want to believe he and humans in general are somehow "higher" on some evolutionary ladder than other species, I have some news for him

THERE IS NO FU*$ING EVOLUTIONARY LADDER.

Humans are neither higher nor lower than any other organisms. This is an antiquated and inane view of evolution. Sure, humans are smart. Sure we are more complex in some aspects than, say, some bacteria. But new features evolve on ALL branches in the tree of life. And some organisms lose features present in their ancestors. The evolution of complexity is, well complex, sure, but please, "higher" and "lower" organisms? An evolutionary ladder? Uggh.

I do not pay much attention to human GWAS studies, but if Wade's understanding of them is akin to his understanding of evolution, well, I would then infer that GWAS studies have revolutionized all of medicine. For his butchering of evolution, I am giving Nicholas Wade my 6th coveted "Twisted tree of life award"

Friday, June 11, 2010

Well, I so wanted to write a piece about the Nature-UC dispute going on right now. In summary, a group from the University of California (University Committee on Library and Scholarly Communication (UCOLASC) including librarians and scientists and various others circulated a letter a few days ago to UC faculty suggesting a possible boycott of Nature journals due in large part to impending price increases. The letter became public (see for example here). Some News stories were written. Some blogs and many tweets were posted (including mine, wondering why I had not heard anything about the whole issue before). Nature responded. UC responded back. More news stories were written (e.g., SJ Mercury news here) and more blogs and tweets came out.

But something was missing in the whole thing from my point of view. What was missing was a discussion of how this whole discussion should not really be about UC vs. Nature. It should be about how the publishing systems right now is broken - about how we should expect commercial publishers to want to make money and how what we need to do as scientists is to take control of publishing to make it more open and to save taxpayer's money because we do not really need many of the broken parts of the publishing system.

And it should not have really been about Nature vs. UC - Nature to me is not the issue here. I personally would not have gone after Nature in the way the UC library group did. Nature does some good things and some bad things. As do many, if not all publishers, even, God forbid, PLoS. Nature in fact has been doing some useful experimenting with some nice web/open science features. We should neither expect them to do good things or bad things. What we need to do is think about the whole system of publishing, not just go after one publisher.

Fortunately, before I wrote this up, I found a blog post that covers many of my feelings on the issue. And it just happens to be by my brother, Michael (CoFounder of PLoS), who is traveling on the East Coast and who I have not had a chance to talk to at all about the Nature-UC issue. So I recommend people go to his post: The Nature kerfuffle: boycott the business model not the price

I am not saying I agree with every sentiment in his post but the key part to me is:

"It’s time for UC to follow suit. Rather than haggling over prices, the faculty, students, staff and administration of all ten UC campuses should unite to end the business practices that empower NPG and other publishes to regularly attempt to extort money from our chronically cash-strapped library system."

I have little to add to this so will leave it there. Read his post for more.

And have gotten some great responses so far from my various social networking circles and I thought I would centralize them here. At the bottom I will post some of the raw responses. Here is a current summary